Context: Head and neck squamous cell carcinoma (HNSCC) has unsatisfactory clinical outcomes, particularly in advanced disease, and epigenetic drugs are being investigated as a way to improve treatment. Histone deacetylase inhibitors such as panobinostat have shown limited efficacy against solid tumours when used alone, which has drawn attention to their combinations with other targeted agents. Histone lysine demethylases (KDMs) of the Jumonji C family are overexpressed in HNSCC, and KDM4A and KDM6B have been implicated in the regulation of pluripotency genes and the promotion of stemness. This dataset comes from an in vitro study that asked whether Jumonji C KDM inhibitors exert anticancer effects in HNSCC cells and whether combining them with panobinostat, or with the DNA methyltransferase inhibitor decitabine, enhances those effects. The results are reported in Dorna D. et al., Experimental Cell Research 460 (2026) 115042, https://doi.org/10.1016/j.yexcr.2026.115042, and the dataset contains the data behind all nine figures of that article.
Models and treatments: Two HNSCC cell lines were used: FaDu (HPV-negative, primary hypopharyngeal carcinoma) and SCC-152 (HPV-positive, recurrent hypopharyngeal carcinoma). Non-tumorigenic HaCaT keratinocytes were included to assess selectivity towards cancer cells. The compounds included the KDM inhibitors GSK-J4 (KDM6), ML324 (KDM4), JIB-04 (KDM4/5/6), and IOX-1, a broad-spectrum inhibitor of 2-oxoglutarate-dependent oxygenases, as well as the pan-histone deacetylase inhibitor panobinostat and the DNA methyltransferase inhibitor decitabine. Treatment concentrations in all subsequent assays were derived from the IC50 values determined in the single-compound viability assay.
Methodology: Cell viability in monolayer culture was measured by resazurin reduction after 48 h of exposure to five-point concentration series, and IC50 values were derived for each compound and cell line. Combinations of each KDM inhibitor with panobinostat were tested in the same assay at the IC50, half and quarter IC50, and decitabine and IOX-1 at a fixed 20 µM; drug interaction was quantified as the Combination Index by the Chou-Talalay method in CompuSyn. Three-dimensional spheroids, formed for four days in ultra-low-attachment plates, were treated for 72 h, assessed by resazurin reduction and imaged after live/dead staining with calcein-AM and propidium iodide. Clonogenic potential was determined after 48 h of treatment at half the IC50, followed by growth in compound-free medium to day 14, with crystal violet staining and colony counting in OpenCFU. Apoptosis was measured by Annexin V / 7-AAD staining and DNA damage by detection of histone H2A.X phosphorylated at Ser139, both on a Muse Cell Analyzer. Transcript levels of stemness-related genes (SOX2, POU5F1, ALDH1A1, ABCG2) and of genes involved in cell cycle regulation, apoptosis and cell adhesion (CDKN1A, CDKN2A, BIRC5, CDH1) were measured by RT-qPCR on a LightCycler 96 and calculated by the Pfaffl method against the reference genes TBP and PBGD. Binding of KDM4A and KDM6B at the promoters of the four stemness-related genes in FaDu cells was determined by chromatin immunoprecipitation followed by qPCR and expressed as (Bound − IgG) / Input. Each assay was performed in at least three independent biological replicates, and differences were assessed by one-way ANOVA with Tukey's post hoc test and by Student's t-test against the vehicle control.
Content and structure: The data are arranged in eight folders, one per assay, numbered in the order of the figures of the article. Within each folder, raw_data holds the primary measurements as produced by the instruments or recorded at the bench: plate-reader fluorescence exports, qPCR quantification cycle (Cq) exports and plate layouts, colony counts, flow cytometry gating plots, and microscope and plate photographs. Folder processed_data holds the per-plate and per-replicate calculation tables in the assays where such a stage exists, and analysis holds the summary tables aggregated across biological replicates together with the curve fitting, synergy analysis and statistical output (the values plotted in the article are always found in analysis). Data tables are provided as Excel workbooks (.xlsx), images as PNG, JPEG and TIFF files, and the CompuSyn output as HTML reports with embedded GIF plots. A README.txt in the root of the dataset describes the cell lines, compounds, treatment concentrations and conventions common to all assays, and a README.txt in each folder documents the method, plate layout, file naming, calculation steps, replicate structure and statistical conventions of that assay.
